Stability Of Helical Structure Research Articles

On the scope of the double Ugi multicomponent stapling to produce helical peptides

The stabilization of helical structures by peptide stapling approaches is now a mature technology capable to provide a variety of biomedical applications. Recently, it was shown that multicomponent macrocyclization is not only an effective way to introduce conformational constraints but it also allows to incorporate additional functionalities to the staple moiety in a one-pot process. This work investigates the scope of the double Ugi multicomponent stapling approach in its capacity to produce helical peptides from unstructured sequences. For this, three different stapling combinations were implemented and the CD spectra of the cyclic peptides were measured to determine the effect of the multicomponent macrocyclization on the resulting secondary structure. A new insight into some structural factors influencing the helicity type and content is provided, along with new prospects on the utilization of this methodology to diversify the molecular tethers linking the amino acid side chains.

Microsolvation of lithium–phosphorus double helix: a DFT study

The chemistry of complexes becomes interesting due to their structural diversity in different environments like in aqueous phase, in gas-phase or in the interior of a host. In the last few decades, powerful tools for the determination of gas-phase have been developed. In this context, the microsolvation approach of Li7P7 helix, where the passage from the bare double-strand helix to the hydrated denatured helix, has been addressed through successive attachment of water molecules using density functional theory. The stability of helical structure of the small clusters has been analyzed on the basis of polar bonding interaction between oxygen end of water molecule and Li centers of the Li7P7 helix. The Li7P7 helix is favored when associated with zero to eight water molecules, but the binding of the ninth water molecule brings a drastic change in the structure. Our results suggest that the natural charges on some sites in Li7P7 are large enough to induce partial and eventually total dissociation of water molecules. We shed light on the bonding situation through natural bond orbital, quantum theory of atoms in molecules and energy decomposition analyses which suggest dominant electrostatic interaction between Li centers of Li7P7 and O centers of water molecules (accounting for 60–64% of total bonding attraction). Nevertheless, 31–36% of total attraction is also originated from the orbital interaction. Variation in reactivity on microhydration is also analyzed. In order to check the site selectivity, we have computed conceptual density functional theory-based local reactivity descriptors such as dual descriptor based on the Fukui function, Δf(r), and multiphilic descriptor based on the philicity, Δω(r).

Quantum theory of helimagnetic thin films

We study properties of a helimagnetic thin film with a quantum Heisenberg spin model by using the Green's-function method. Surface spin configuration is calculated by minimizing the spin interaction energy. It is shown that the angles between spins near the surface are strongly modified with respect to the bulk configuration. Taking into account this surface spin reconstruction, we calculate self-consistently the spin-wave spectrum and the layer magnetizations as functions of temperature up to the disordered phase. The spin-wave spectrum shows the existence of a surface-localized branch which causes a low surface magnetization. We show that quantum fluctuations give rise to a crossover between the surface magnetization and interior-layer magnetizations at low temperatures. We calculate the transition temperature and show that it depends strongly on the helical angle. Results are in agreement with existing experimental observations on the stability of helical structure in thin films and on the insensitivity of the transition temperature with the film thickness. We also study effects of various parameters such as surface exchange and anisotropy interactions. Monte Carlo simulations for the classical spin model are also carried out for comparison with the quantum theoretical result.

Emergence of structure through protein–protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins

Human centrosomal proteins show a significant, 3.5 fold, bias to be both unstructured and coiled-coils with respect to generic human proteins, based on results from state of the art bioinformatics tools. We hypothesize that this bias means that these proteins adopt an ensemble of disordered and partially helical conformations, with the latter becoming stabilized when these proteins form complexes. Characterization of the structural properties of 13 peptides from 10 different centrosomal proteins ranging in size from 20 to 61 residues by biophysical methods led us to confirm our hypothesis in most cases. Interestingly, the secondary structure adopted by most of these peptides becomes stabilized at acidic pH and it is concentration dependent. For two of them, PIK3R1453–513 and BRCA11253–1273, we observed not only the stabilization of helical structure through self-association, but also the presence of β-structures linked to the formation of high molecular weight oligomers. These oligomers are the predominant forms detected by CD, but unobservable by liquid state NMR. BRCA11397–1424 and MAP3K11396–441 populate helical structures that can also self-associate at pH3 through oligomeric species. Four peptides, derived from three proteins, namely CCNA2103–123, BRCA11253–1273, BRCA11397–1424 and PIK3R1453–513, can form intermolecular associations that are concomitant with alpha or beta structure stabilization. The self-phosphorylation previously described for the kinase NEK2 did not lead to any stabilization in the peptide's structure of NEK2303–333, NEK2341–361, and NEK2410–430. Based on these results, obtained from a series of peptides derived from a significant number of different centrosomal proteins, we propose that conformational polymorphism, modulated by intermolecular interactions is a general property of centrosomal proteins.

Energetic Frustration of Apomyoglobin Folding: Role of the B Helix

Apomyoglobin folds by a sequential mechanism in which the A, G, and H helix regions undergo rapid collapse to form a compact intermediate onto which the central portion of the B helix subsequently docks. To investigate the factors that frustrate folding, we have made mutations in the N-terminus of the B helix to stabilize helical structure (in the mutant G23A/G25A) and to promote native-like hydrophobic packing interactions with helix G (in the mutant H24L/H119F). The kinetic and equilibrium intermediates of G23A/G25A and H24L/H119F were studied by hydrogen exchange pulse labeling and interrupted hydrogen/deuterium exchange combined with NMR. For both mutants, stabilization of helical structure in the N-terminal region of the B helix is confirmed by increased exchange protection in the equilibrium molten globule states near pH 4. Increased protection is also observed in the GH turn region in the G23A/G25A mutant, suggesting that stabilization of the B helix facilitates native-like interactions with the C-terminal region of helix G. These interactions are further enhanced in H24L/H119F. The kinetic burst phase intermediates of both mutants show increased protection, relative to wild-type protein, of amides in the N-terminus of the B helix and in part of the E helix. Stabilization of the E helix in the intermediate is attributed to direct interactions between E helix residues and the newly stabilized N-terminus of helix B. Stabilization of native packing between the B and G helices in H24L/H119F also favors formation of native-like interactions in the GH turn and between the G and H helices in the ensemble of burst phase intermediates. We conclude that instability at the N-terminus of the B helix of apomyoglobin contributes to the energetic frustration of folding by preventing docking and stabilization of the E helix.

Synthesis of β‐Peptides with β‐Helices from New C‐Linked Carbo‐β‐Amino Acids: Study on the Impact of Carbohydrate Side Chains

The design and synthesis of beta-peptides from new C-linked carbo-beta-amino acids (beta-Caa) presented here, provides an opportunity to understand the impact of carbohydrate side chains on the formation and stability of helical structures. The beta-amino acids, Boc-(S)-beta-Caa((g))-OMe 1 and Boc-(R)-beta-Caa((g))-OMe 2, having a D-galactopyranoside side chain were prepared from D-galactose. Similarly, the homo C-linked carbo-beta-amino acids (beta-hCaa); Boc-(S)-beta-hCaa((x))-OMe 3 and Boc-(R)-beta-hCaa((x))-OMe 4, were prepared from D-glucose. The peptides derived from the above monomers were investigated by NMR, CD, and MD studies. The beta-peptides, especially the shorter ones obtained from the epimeric (at the amine stereocenter C(beta)) 1 and 2 by the concept of alternating chirality, showed a much smaller propensity to form 10/12-helices. This substantial destabilization of the helix could be attributed to the bulkier D-galactopyranoside side chain. Our efforts to prepare peptides with alternating 3 and 4 were unsuccessful. However, the beta-peptides derived from alternating geometrically heterochiral (at C(beta)) 4 and Boc-(R)-beta-Caa((x))-OMe 5 (D-xylose side chain) display robust right-handed 10/12-helices, while the mixed peptides with alternating 4 and Boc-beta-hGly-OMe 6 (beta-homoglycine), resulted in left-handed beta-helices. These observations show a distinct influence of the side chains on helix formation as well as their stability.

Stabilization of Folded Peptide and Protein Structures via Distance Matching with a Long, Rigid Cross-Linker

Intramolecular cross-linking is predicted to stabilize the folded state of peptides and proteins most effectively if the cross-linker provides a rigid link that is well-matched in end-to-end distance with attachment sites in the peptide or protein. We describe a thiol-reactive sulfonated alkyne-based cross-linker that is demonstrably more effective than more flexible counterparts. Exceptional stabilization of helical structure in short peptides is obtained.

Abundant graft chains do not influence coil-to-helix but α-to-β transition of polylysine backbone, resulting in thermoreversible β-to-α transition

We have demonstrated that cationic comb-type copolymers (PLL- g-Dex) consisting of a cationic polylysine backbone and abundant grafts of water-soluble polymers stabilize DNA hybrids. Furthermore, the copolymers were found to accelerate the strand exchange reaction between a double-stranded DNA and its complementary single-stranded DNA. In this study, we investigated pH-induced coil-to-helix and temperature-induced α-to-β transition of PLL- g-Dex to evaluate the effect of the graft chains on conformation of the polylysine backbone. The coil-to-helix transition was hardly influenced by the grafted dextran. The copolymer having 24 mol% (93 wt%) dextran still underwent coil-to-helix transition. No change in transition pH with dextran grafting density of the copolymer was observed. In contrast to the coil-to-helix transition, the dextran grafts impacted the temperature-induced α-to-β transition. The graft chains even at 1 mol% (38 wt%) affected α-to-β transition of the PLL backbone. The transition temperature increased from 45°C to 77 °C by 11 mol% (88 wt%) dextran grafting, resulted in stabilization of helical structure at the higher temperature. Furthermore, thermoreversible β-to-α transition of the copolymer was observed for the copolymer with a particular grafting degree. The grafted dextran seemingly modified inter-strands or inter-segments interactions of the polylysine backbones which are required for β-sheet assembling.

Twist of cholesteric liquid crystal cells: Stability of helical structures and anchoring energy effects

We consider helical configurations of a cholesteric liquid crystal (CLC) sandwiched between two substrates with homogeneous director orientation favored at both confining plates. We study the CLC twist wave number q characterizing the helical structures in relation to the free twisting number q(0) which determines the equilibrium value of CLC pitch P(0) = 2 pi/ q(0) . We investigate the instability mechanism underlying transitions between helical structures with different spiral half-turn numbers. Stability analysis shows that for equal finite anchoring strengths this mechanism can be dominated by in-plane director fluctuations. In this case the metastable helical configurations are separated by the energy barriers and the transitions can be described as the director slippage through these barriers. We extend our analysis to the case of an asymmetric CLC cell in which the anchoring strengths at the two substrates are different. The asymmetry introduces two qualitatively different effects: (a) the intervals of twist wave numbers representing locally stable configurations with adjacent helix half-turn numbers are now separated by instability gaps; and (b) sufficiently large asymmetry, when the difference between azimuthal anchoring extrapolation lengths exceeds the thickness of the cell, will suppress the jumplike behavior of the twist wave number.

High affinity RNase S-peptide variants obtained by phage display have a novel "hot-spot" of binding energy.

Using phage display mutagenesis, high affinity variants of RNase S-peptide were produced that bind to RNase S-protein over 100-fold more tightly than the wild type S-peptide. The S-peptide: S-protein interface was further characterized using "biased" phage display libraries, where each targeted residue was constrained to be either polar or nonpolar. The use of these tailored libraries placed constraints on the type of interactions present during affinity maturation process and allowed more amino acids to be randomized simultaneously. These results, in conjunction with kinetic association and dissociation constants determined by surface plasmon resonance (SPR), highlight the role of a single mutation (A5W) in increasing S-peptide binding affinity. High affinity S-peptide variants were only identified when tryptophan was present in the phage display library at position 5, suggesting that this residue is a "hot-spot" of binding energy in the high affinity variants. Analysis of SPR data in the presence of denaturant suggests that the increased affinity is a result of increased hydrophobic interactions in the transition state rather than a stabilization of helical structure.

NMR Analysis of a Conformational Transition in an Acyclic Peptide. Model System for Studying Helix Unfolding

The stabilization of helical structures in short apolar peptides is readily achieved by introduction of α,α-dialkylamino acids. The use of stereochemically constrained residues in conjunction with conformationally flexible segments permits the design of peptides that are poised to undergo structural transitions. The octapeptide Boc-Leu-Ac8c-Val-Gly-Gly-Leu-Ac8c-Val-OMe (Ac8c = 1-aminocyclooctane-1-carboxylic acid) incorporates residues with contradictory conformational tendencies. NMR analysis in CDCl3, using nuclear Overhauser effects and delineation of hydrogen-bonded NH groups establishes a 310-helical conformation. In a polar strongly solvating medium, like DMSO, the helix unfolds. Studies in CDCl3/DMSO mixtures provide clear evidence for a solvent dependent conformational transition. Amide NH chemical shifts and temperature coefficients at varying solvent composition allow a detailed structural analysis of the unfolding process. The intrinsic fragility of the octapeptide helix provides an opportunity to examine invasion of the helix backbone by water molecules. Studies in DMSO solution containing low concentrations of water establish that preferential water peptide interactions may indeed be present.

Stabilization of helical domains in short peptides using hydrophobic interactions.

The contribution of hydrophobic interactions in the stabilization of helical structure was compared for a series of short peptides that incorporated two epsilon-(3,5-dinitrobenzoyl)Lys residues at various positions. Results showed that in aqueous/organic mixtures, methanol induced helical stability over a wider range and at higher concentration than trifluoroethanol (TFE); a similar degree of stability was seen in low mole fraction mixtures of TFE in water. Solvent mixture titrations in TFE/water demonstrated that helical stability was highest for the peptide having a pair of modified residues spaced by three other residues. Solvent mixture titrations in TFE/water appear to be useful in indicating the degree of hydrophobic stabilization.

Stabilization of helical structure in two 17‐residue amphipathic analogues of the C‐terminal peptide of cytochrome c

The conformations of two 17-residue peptide analogues derived from the C-terminal sequence of pigeon cytochrome c (native sequence = KAERADLIAYLKQATAK) were examined in aqueous and lipid environments by CD spectroscopy. The two analogues, KKLLKKLIAYLKQATAK (K peptide) and EELLEELIAYLKQATAK (E peptide), were made amphipathic with respect to helical segregation by substituting a 6-residue sequence at the N-terminus of the native peptide. Their structures were compared to the native peptide under aqueous conditions of varying pH and temperature, and in the presence of liposomes composed of phosphatidylcholine and phosphatidylserine in the ratio of 9:1. The results indicated that the native peptide remains unstructured under all the conditions examined even though this region of the native molecule is surface exposed and helical. The E peptide, however, was helical under aqueous conditions at 25 degrees C from pH 2-10 with a maximum helicity at pH 4 (54% helix from analysis of CD data). The ellipticity of the E peptide at pH 4 and 8 was concentration dependent, indicating an aggregation phenomenon. In studies in which the CD spectrum was measured at different temperatures, the E peptide became more helical at lower temperatures at pH 4 but not at pH 8. Upon interaction with a lipid membrane in the form of liposomes, there appeared to be a slight destabilization in the structure of the E peptide. The K peptide in an aqueous environment behaved like the native peptide in that it was structureless at all pHs and temperatures examined. In the presence of liposomes, however, this peptide had a high helical content (75% helix from analysis of CD data). These findings suggest that while stabilization of the helix dipole with negative charges at the N-terminus are important in inducing helical conformation in the E peptide, hydrophobic interactions created during aggregation appear to provide the principal stabilizing force. The results with the K peptide demonstrate that the positive N-terminal sequence of this peptide is able to interact with the negatively charged head groups in the phospholipid membrane in such a fashion as to stabilize a helical structure that is not apparent in an aqueous environment alone.

The role of solvents in the stabilization of helical structure: the low pH ribo A8 and A10 double helices in mixed solvents.

The order-disorder transitions of the double helices formed by the ribo-oligoadenylic acids rA8 and rA10 at pH 4.2 have been investigated in a series of organic/aqueous mixed solvents. Melting temperature data, Tm, derived from the uv melting curves were used to define the stability of the double helices in the different mixed solvent systems. It was found that the extent of helix destabilization depended in a predictable fashion on both the quantity and the nature of the added organic solvents. For the C1 through C4 aliphatic alcohols, the longer, less branched alcohols proved to be more effective destabilizers of the helical structure. Significantly, the amides proved to be more powerful destabilizers than the alcohols. Analysis of the melting curves provided the Van't Hoff enthalpy change for each transition. The data are interpreted in terms of the role of solvent in the stabilization of ribonucleic acid structure.

Hadamard Stability of Uniform Helical Structures

ABSTRACT We present an analysis of the Hadamard stability of helical structures and find the sufficient stability design criteria. We employ a compact 3(n + 1) dimensional vector space for uniform helical structures and arrive at the governing inequality by employing the traditional Hadamard stability criterion.